WGS based analysis of acquired antimicrobial resistance in human and non-human Acinetobacter baumannii isolates from a German perspective

Integrating Genomic Data into Public Health Surveillance for Multidrug-Resistant Organisms, Washington, USA

Mitigating antimicrobial resistance (AMR) is a public health priority to preserve antimicrobial treatment options. The Washington State Department of Health in Washington, USA, piloted a process to leverage longitudinal genomic surveillance on the basis of whole-genome sequencing (WGS) and a genomics-first cluster definition to enhance AMR surveillance. Here, we outline the approach to collaborative surveillance and describe the pilot using 6 carbapenemase-producing organism outbreaks of 3 species: Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. We also highlight how we applied the approach to an emerging outbreak. We found that genomic and epidemiologic data define highly congruent outbreaks. By layering genomic and epidemiologic data, we refined linkage hypotheses and addressed gaps in traditional epidemiologic surveillance. With the accessibility of WGS, public health agencies must leverage new approaches to modernize surveillance for communicable diseases.

Comprehensive molecular epidemiology of Acinetobacter baumannii from diverse sources in Nigeria

BACKGROUND

Acinetobacter baumannii, a Gram-negative bacterium, is a public health threat due to its role in nosocomial infections and increasing antibiotic resistance. In Nigeria, data on the molecular epidemiology of A. baumannii is scarce. This study investigates the genetic diversity and the presence of antimicrobial resistance determinants and virulence-related genes in whole-genome sequencing data of 189 Nigerian A. baumannii isolates deposited in public repositories. Genotypes were determined in-silico by multilocus sequence typing (MLST) and core genome MLST (cgMLST). Further, antimicrobial resistance (AMR) and virulence-related genes were analyzed.

RESULTS

Most isolates (57.67%) originated from South-west Nigeria. Isolates of human origin accounted for 33.86%, while environmental sources comprised 6.87%, and 59.27% lacked information on the source of isolation. The cgMLST analysis revealed a multitude of genomic lineages circulating in Nigeria. The MLST Oxford scheme identified 44 sequence types (STs) in 62.96% of strains, with ST1089 being the most prevalent. The MLST Pasteur could assign 95.77% of strains to 49 STs, with ST2(IC2) and ST85(IC9) being the most dominant. Antimicrobial resistance analysis detected 168 genes encoding resistance to 12 antibiotic classes, with cephalosporin, carbapenem, and aminoglycoside resistance genes being the most prevalent. Notably, blaADC-79 (23.81%), blaOXA-23 (30.69%), and aph(3″)-Ib (30%) were frequent variants encountered. Seventeen multi-efflux system genes conferring resistance to multiple antibiotic classes were identified. Virulence gene analysis revealed 137 genes encoding six mechanisms, with genes for nutritional factors, effector delivery systems, and biofilm production being the most prevalent.

CONCLUSION

This study highlights the diversity in AMR and virulence genes of A. baumannii in Nigeria, emphasizing the need for ongoing genomic surveillance to inform infection control and develop antibiotic resistance management strategies.

Prevalence and Antibiogram Pattern of Acinetobacter baumannii from 2013 to 2023 in a Tertiary Care Hospital in the Western Region of Saudi Arabia

Acinetobacter baumannii is pathogen of global concern. It causes infection, especially among immunocompromised individuals in intensive care units, due to its ability to survive for long periods on hard surfaces and under a wide range of environmental conditions and become resistant to almost all the available antibiotics used in clinical practice. Objectives: This study aims to address the gap in A. baumannii surveillance in Saudi Arabia by tracking the prevalence, patterns, and trends of acquired A. baumannii resistance at a healthcare facility in the western part of Saudi Arabia over eleven years. Methods: The study was conducted in a tertiary care hospital in the western region of Saudi Arabia, from January 2013 to December 2023. Results: Our data indicated that A. baumannii infections were predominantly observed in inpatients admitted to the hospital (96%) compared to those treated as outpatients in the emergency clinic (4%). The mean of annual A. baumannii infections isolated from inpatients is 503.3, whereas the mean for outpatients is 21, indicating a statistically significant difference with a p-value of <0.0001. The analysis of the antimicrobial susceptibility profile of A. baumannii demonstrated a variable levels of resistance to the evaluated antibiotics. The lowest resistance rate was for colistin. Conclusions: In conclusion, the incidence patterns of A. baumannii isolates peaked in 2013, then declined, and have recently shown an increase, underscoring the necessity for proactive interventions to curtail its dissemination, notwithstanding initial decreases in infection rates and resistance.

Whole genome sequencing characterization and comparative genome analysis of Acinetobacter baumannii JJAB01: A comprehensive insights on antimicrobial resistance and virulence genotype

The emergence of antibiotic resistance has significantly elevated the threat posed by Acinetobacter baumannii as an opportunistic pathogen. A.baumannii, a notorious bacterium, poses a serious threat to health care, leading to severe nosocomial infections, particularly in immunocompromised individuals. Whole-Genome Sequencing studies are efficient in providing accurate genetic information, aiding in detecting outbreaks, surveillance of resistance, and controlling infection transmission. In this study, we investigated the whole genome of a clinical isolate A. baumannii JJAB01 which sourced from a urine sample of an Intensive Care Unit (ICU) patient. This strain showed resistance to 24 available antibiotics, signifying Extremely Drug Resistant (XDR) and high potential for pathogenicity. Whole Genome Sequencing was performed using Illumina, and the raw reads were evaluated using the FastQC tool. Genome assembly and annotation were performed with Unicycler and the RAST server. The JJAB01 genome is 4.07 Mb with a GC content of 38.9 %. A total of 51 and 31 virulence factors and antimicrobial-resistant (AMR) genes were predicted using the VFDB and CARD databases. Comparative genome studies were carried out on virulence factors, resistance genes, prophages, and Multi-Locus Sequence Typing (MLST) across twelve closely related A. baumannii genomes, including JJAB01, X4-584, X4-705, 2023CK-00423, 2023CK-00890, 2023CK-00127, 2022CK-00066, B20AB01, B20AB10, F20AB03, G20AB08, and X4-65. These computational investigations in this study emphasis the multidimensional nature of the ICU strain JJAB01 and its genetic similarity to other strains, thereby enhancing our understanding of drug resistance and the pathogenicity associated with A. baumannii infections.

Whole genome analysis revealed the role of blaOXA-23 and blaOXA-66 genes in carbapenem resistance of Acinetobacter baumannii strains

Acinetobacter baumannii is a multidrug-resistant bacterium that has emerged as a significant nosocomial pathogen globally and renowned for its ability to acquire antimicrobial resistance (AMR) genes. However, understanding of its resistance mechanisms to certain drug classes remains limited. This study focused on four bacterial strains (AB863, AB889, AB930, and AB960) exhibiting carbapenem resistance. They demonstrated high minimum inhibitory concentration (MIC) (128 mg/L) to meropenem and were categorized as extensively drug-resistant strains. Subsequently, they were identified as A. baumannii through 16S rRNA gene sequence analysis and species-specific PCR targeting the blaOXA51-like gene. Three strains were sequenced for their genomes to study the genetic determinants and functional relevance of carbapenem resistance. The draft genome length of the strains ranged from 3.8 to 4.0 Mbp. A total of 16 antibiotic resistance genes including the genes blaOXA-23 and blaOXA-66 which mediate carbapenem resistance were identified in the genomes. A comprehensive multilocus sequence typing analysis involving 95 A. baumannii strains from different Asian countries assigned the four strains to sequence type 2 (ST2), the most predominant ST circulating in Asia. Comparative genome analysis also revealed blaOXA-66 as the most dominant variant of blaOXA-51-like gene and also a widespread distribution of blaOXA-23 gene. In addition, various mobile genetic elements associated with AMR genes and three efflux pumps families were detected in the genomes of the strains. Transformation of blaOXA-23 and blaOXA-66 genes resulted in meropenem resistance in the transformant which exhibited a MIC of 2 mg/L, thus confirming direct involvement of both genes in carbapenem resistance.

Comparative genomic and phenotypic analysis of low- and high-virulent Acinetobacter baumannii strains: Insights into antimicrobial resistance and virulence potential

Multi-drug resistant Acinetobacter baumannii poses a significant threat to public health. This study investigated the genomic features and phenotypic characteristics of two clinical A. baumannii strains, KBN10P01317 (low-virulent) and KBN10P01599 (high-virulent), which share the same sequence type and antimicrobial susceptibility profile. The phenotypic characteristics of A. baumannii strains were assessed by antimicrobial susceptibility testing and virulence trait examination in vitro and in vivo. Whole-genome sequencing was conducted for comparative genomic analysis, and the expression of virulence-associated genes was analyzed using quantitative polymerase chain reaction. Our comparative genomic analysis revealed that KBN10P01599 harbored a larger genome with a greater number of antimicrobial resistance genes, including two copies of the critical resistance gene blaOXA-23, which might contribute to its higher minimum inhibitory concentration for carbapenems (64 μg/ml) compared to KBN10P01317 (32 μg/ml). Although both A. baumannii strains possessed the same repertoire of virulence-associated genes, KBN10P01599 exhibited significantly enhanced expression of quorum sensing (abaI/R) and biofilm formation genes (csuCDE, bap, and pgaA), correlating with its virulence traits, including increased surface motility, biofilm formation, and adherence to host cells. The differences in the expression of virulence-associated genes between the two strains were partly attributed to the transposition of insertion sequence elements. These findings provide valuable insights into the genetic basis of the virulence potential and antimicrobial resistance in A. baumannii, highlighting the evolutionary changes that may occur within strains of the same clone.

Epidemiological and Clinical Insights into Acinetobacter baumannii: A Six-Year Study on Age, Antibiotics, and Specimens

Background

This six-year retrospective study provides an in-depth analysis of the epidemiological and clinical patterns associated with Acinetobacter baumannii (A. baumannii) infections, focusing on age distribution, antibiotic resistance profiles, and specimen types.

Aim

The research examines the incidence and characteristics of both non-Multi-Drug Resistant (non-MDR) and Multi-Drug Resistant (MDR) A. baumannii strains by reviewing patient records from January 2016 to December 2022.

Methods

Through a statistical analysis, the study highlights the incidence rates across diverse age groups and explores the impact of antibiotic treatment regimens on infection outcomes. Additionally, it identifies the primary clinical specimen types for each strain, noting an association between non-MDR A. baumannii and midstream urine samples, while MDR A. baumannii strains were more frequently found in respiratory, wound, peripheral, and central line swaps/specimens.

Results

The results indicate that in 2016, non-MDR A. baumannii infections were notably more frequent compared to MDR A. baumannii cases. However, a significant shift occurred in 2021 and 2022, with a marked decrease in non-MDR A. baumannii cases and an increase in MDR A. baumannii infections. Antibiotic susceptibility testing revealed that non-MDR strains were commonly tested against cefazolin, ceftazidime, ciprofloxacin, gentamicin, nitrofurantoin, oxacillin, piperacillin/tazobactam, and trimethoprim/sulfamethoxazole. In contrast, MDR strains were frequently tested against amikacin, cefepime, colistin, meropenem, imipenem, and tigecycline.

Conclusion

This study enhances the understanding of A. baumannii clinical behaviour and resistance patterns, offering valuable insights to support future research and inform strategies for infectious disease management and control.

Artificial intelligence in predicting pathogenic microorganisms' antimicrobial resistance: challenges, progress, and prospects

The issue of antimicrobial resistance (AMR) in pathogenic microorganisms has emerged as a global public health crisis, posing a significant threat to the modern healthcare system. The advent of Artificial Intelligence (AI) and Machine Learning (ML) technologies has brought about revolutionary changes in this field. These advanced computational methods are capable of processing and analyzing large-scale biomedical data, thereby uncovering complex patterns and mechanisms behind the development of resistance. AI technologies are increasingly applied to predict the resistance of pathogens to various antibiotics based on gene content and genomic composition. This article reviews the latest advancements in AI and ML for predicting antimicrobial resistance in pathogenic microorganisms. We begin with an overview of the biological foundations of microbial resistance and its epidemiological research. Subsequently, we highlight the main AI and ML models used in resistance prediction, including but not limited to Support Vector Machines, Random Forests, and Deep Learning networks. Furthermore, we explore the major challenges in the field, such as data availability, model interpretability, and cross-species resistance prediction. Finally, we discuss new perspectives and solutions for research into microbial resistance through algorithm optimization, dataset expansion, and interdisciplinary collaboration. With the continuous advancement of AI technology, we will have the most powerful weapon in the fight against pathogenic microbial resistance in the future.

Investigating an outbreak of extensively drug-resistant Acinetobacter baumannii in a tertiary healthcare centre in lebanon using next-generation sequencing

The frequent occurrence of Acinetobacter baumannii in hospital settings and the elevated rate of antimicrobial resistance in this pathogen represent a serious clinical and public health threat worldwide, and particularly in Lebanon where outbreak surveillance and control are still insufficient. Whole-genome sequencing (WGS) is a fast and reliable tool to study outbreaks at the molecular level and obtain actionable knowledge, leading to better control measures. A total of 59 A. baumannii isolates were collected from intensive care unit (ICU) patients (57 isolates) and from the hospital environment (2 isolates) between August 2022 and May 2023, antimicrobial susceptibility testing (AST) was performed and gDNA was subjected to WGS. Analysis was performed to reveal the sequence types (ST), the relatedness to strains that caused other outbreaks and the arsenal of resistance genes harboured by these bacteria. Of 59 isolates, 85% were categorised as extensively drug-resistant (XDR), 13.6% as multidrug-resistant (MDR) and 1.7% as pan-drug-resistant. All isolates belonged to international clone (IC)2, of which the majority were of ST2 (91.5%). The isolates clustered well with those of a previous outbreak in the same hospital. In addition, isolates from hospitals in Lebanon clustered well together and some clustered with those originating from other countries. The observed genetic relatedness between the current isolates and those from the previous outbreaks underscores the importance of strict surveillance to limit the threat of outbreaks. Moreover, the clustering of isolates from Lebanon with others from distant countries proves the necessity to further investigate the international spread of drug-resistant pathogens and the implementation of control strategies.

Detection of florfenicol resistance in opportunistic Acinetobacter spp. infections in rural Thailand

Florfenicol (Ff) is an antimicrobial agent belonging to the class amphenicol used for the treatment of bacterial infections in livestock, poultry, and aquaculture (animal farming). It inhibits protein synthesis. Ff is an analog of chloramphenicol, an amphenicol compound on the WHO essential medicine list that is used for the treatment of human infections. Due to the extensive usage of Ff in animal farming, zoonotic pathogens have developed resistance to this antimicrobial agent. There are numerous reports of resistance genes from organisms infecting or colonizing animals found in human pathogens, suggesting a possible exchange of genetic materials. One of these genes is floR, a gene that encodes for an efflux pump that removes Ff from bacterial cells, conferring resistance against amphenicol, and is often associated with mobile genetic elements and other resistant determinants. In this study, we analyzed bacterial isolates recovered in rural Thailand from patients and environmental samples collected for disease monitoring. Whole genome sequencing was carried out for all the samples collected. Speciation and genome annotation was performed revealing the presence of the floR gene in the bacterial genome. The minimum inhibitory concentration (MIC) was determined for Ff and chloramphenicol. Chromosomal and phylogenetic analyses were performed to investigate the acquisition pattern of the floR gene. The presence of a conserved floR gene in unrelated Acinetobacter spp. isolated from human bacterial infections and environmental samples was observed, suggesting multiple and independent inter-species genetic exchange of drug-resistant determinants. The floR was found to be in the variable region containing various mobile genetic elements and other antibiotic resistance determinants; however, no evidence of HGT could be found. The floR gene identified in this study is chromosomal for all isolates. The study highlights a plausible impact of antimicrobials used in veterinary settings on human health. Ff shares cross-resistance with chloramphenicol, which is still in use in several countries. Furthermore, by selecting for floR-resistance genes, we may be selecting for and facilitating the zoonotic and reverse zoonotic exchange of other flanking resistance markers between human and animal pathogens or commensals with detrimental public health consequences.

Draft genome sequence of Acinetobacter baumannii Ab10, a clinical isolate from Hospital University Sains Malaysia (HUSM), Malaysia

Acinetobacter baumannii strain Ab10 retrieved in Malaysia in 2017 represents a pathogen carrying multiple antibiotic-resistant genes (blaOXA-23, ant(3")-Ila, blaADC-32, and blaOXA-699). We introduce the 3.89 Mbp genome sequence from short-read sequencing (Illumina's NovaSeq6000).

Insights into the Microbiome and Antibiotic Resistance Genes from Hospital Environmental Surfaces: A Prime Source of Antimicrobial Resistance

Hospital environmental surfaces are potential reservoirs for transmitting hospital-associated pathogens. This study aimed to profile microbiomes and antibiotic resistance genes (ARGs) from hospital environmental surfaces using 16S rRNA amplicon and metagenomic sequencing at a tertiary teaching hospital in Malaysia. Samples were collected from patient sinks and healthcare staff counters at surgery and orthopaedic wards. The samples' DNA were subjected to 16S rRNA amplicon and shotgun sequencing to identify bacterial taxonomic profiles, antibiotic resistance genes, and virulence factor pathways. The bacterial richness was more diverse in the samples collected from patient sinks than those collected from staff counters. Proteobacteria and Verrucomicrobia dominated at the phylum level, while Bacillus, Staphylococcus, Pseudomonas, and Acinetobacter dominated at the genus level. Staphylococcus epidermidis and Staphylococcus aureus were prevalent on sinks while Bacillus cereus dominated the counter samples. The highest counts of ARGs to beta-lactam were detected, followed by ARGs against fosfomycin and cephalosporin. We report the detection of mcr-10.1 that confers resistance to colistin at a hospital setting in Malaysia. The virulence gene pathways that aid in antibiotic resistance gene transfer between bacteria were identified. Environmental surfaces serve as potential reservoirs for nosocomial infections and require mitigation strategies to control the spread of antibiotic resistance bacteria.

Antimicrobial Resistance in Romania: Updates on Gram-Negative ESCAPE Pathogens in the Clinical, Veterinary, and Aquatic Sectors

Multidrug-resistant Gram-negative bacteria such as Acinetobacter baumannii, Pseudomonas aeruginosa, and members of the Enterobacterales order are a challenging multi-sectorial and global threat, being listed by the WHO in the priority list of pathogens requiring the urgent discovery and development of therapeutic strategies. We present here an overview of the antibiotic resistance profiles and epidemiology of Gram-negative pathogens listed in the ESCAPE group circulating in Romania. The review starts with a discussion of the mechanisms and clinical significance of Gram-negative bacteria, the most frequent genetic determinants of resistance, and then summarizes and discusses the epidemiological studies reported for A. baumannii, P. aeruginosa, and Enterobacterales-resistant strains circulating in Romania, both in hospital and veterinary settings and mirrored in the aquatic environment. The Romanian landscape of Gram-negative pathogens included in the ESCAPE list reveals that all significant, clinically relevant, globally spread antibiotic resistance genes and carrying platforms are well established in different geographical areas of Romania and have already been disseminated beyond clinical settings.

Acinetobacter baumannii from Samples of Commercially Reared Turkeys: Genomic Relationships, Antimicrobial and Biocide Susceptibility

Acinetobacter baumannii is especially known as a cause of nosocomial infections worldwide. It shows intrinsic and acquired resistances to numerous antimicrobial agents, which can render the treatment difficult. In contrast to the situation in human medicine, there are only few studies focusing on A. baumannii among livestock. In this study, we have examined 643 samples from turkeys reared for meat production, including 250 environmental and 393 diagnostic samples, for the presence of A. baumannii. In total, 99 isolates were identified, confirmed to species level via MALDI-TOF-MS and characterised with pulsed-field gel electrophoresis. Antimicrobial and biocide susceptibility was tested by broth microdilution methods. Based on the results, 26 representative isolates were selected and subjected to whole-genome sequencing (WGS). In general, A. baumannii was detected at a very low prevalence, except for a high prevalence of 79.7% in chick-box-papers (n = 118) of one-day-old turkey chicks. The distributions of the minimal inhibitory concentration values were unimodal for the four biocides and for most of the antimicrobial agents tested. WGS revealed 16 Pasteur and 18 Oxford sequence types, including new ones. Core genome MLST highlighted the diversity of most isolates. In conclusion, the isolates detected were highly diverse and still susceptible to many antimicrobial agents.

Genomic Determinants of Pathogenicity and Antimicrobial Resistance of Nosocomial Acinetobacter baumannii Clinical Isolates of Hospitalized Patients (2019-2021) from a Sentinel Hospital in Hangzhou, China

Purpose

Acinetobacter baumannii (A. baumannii or AB) is one of the most opportunistic, nosocomial pathogens threatening public healthcare across countries. A. baumannii has become a primary growing concern due to its exceptional ability to acquire antimicrobial resistance (AMR) to multiple antimicrobial agents which is increasingly reported and more prevalent every year. Therefore, there is an urgent need to evaluate the AMR knowledge of A. baumannii for effective clinical treatment of nosocomial infections. This study aimed to investigate the clinical distribution AMR phenotypes and genotypes, and genomic characteristics of A. baumannii isolates recovered from hospitalized patients of different clinical departments of a sentinel hospital to improve clinical practices.

Methods

A total of 123 clinical isolates were recovered from hospitalized patients of different clinical departments during 2019-2021 to analyze AMR patterns, and further subjected to whole-genome sequencing (WGS) investigations. Multi-locus sequence typing (MLST), as well as the presence of antimicrobial-resistant genes (ARGs), virulence factor genes (VFGs) and insertion sequences (ISs) were also investigated from WGS data.

Results

The results highlighted that A. baumannii clinical isolates had shown a high AMR rate, particularly from the intensive care unit (ICU), towards routinely used antimicrobials, ie, β-lactams and fluoroquinolones. ST2 was the most prevalent ST in the clinical isolates, it was strongly associated to the resistance of cephalosporins and carbapenems, with bla_OXA-23 and bla_OXA-66 being the most frequent determinants; moreover, high carrier rate of VFGs was also observed such as all strains containing the ompA, adeF, pgaC, lpsB, and bfmR genes.

Conclusion

Acinetobacter baumannii clinical isolates are mostly ST2 with high rates of drug resistance and carrier of virulence factors. Therefore, it requires measurements to control its transmission and infection.

Carbapenem resistance gene crisis in A. baumannii: a computational analysis

Acinetobacter baumannii (A. baumannii) is one of the members of ESKAPE bacteria which is considered multidrug resistant globally. The objective of this study is to determine the protein docking of different antibiotic resistance gene (ARGs) in A. baumannii. In silico analysis of antibiotic resistance genes against carbapenem are the blaOXA-51, blaOXA-23, blaOXA-58, blaOXA-24, blaOXA-143, NMD-1 and IMP-1 in A. baumannii. The doripenem, imipenem and meropenem were docked to blaOXA-51 and blaOXA-23 using PyRx. The top docking energy was -5.5 kcal/mol by imipenem and doripenem and meropenem showed a binding score of -5. 2 kcal/mol each and blaOXA-23 energy was -4.3 kcal/mol by imipenem and meropenem showed a binding score of -2.3 kcal/mol, while doripenem showed the binding score of -3.4 kcal/mol. Similarly, doripenem imipenem and meropenem were docked to blaOXA-58, IMP-1, Rec A and blaOXA-143, with docking energy was -8.8 kcal/mol by doripenem and meropenem each while imipenem showed a binding score of -4.2 kcal/mol and with IMP-1 demonstrated their binding energies. was -5.7 kcal/mol by meropenem and doripenem showed a binding score of -5.3 kcal/mol, while imipenem showed a binding score of -4.5 kcal/mol. And docking energy was -4.9 kcal/mol by imipenem and meropenem showed binding energy of -3.6 kcal/mol each while doripenem showed a binding score of -3.9 kcal/mol in RecA and with blaOXA-143 docking energy was -3.0 kcal/mol by imipenem and meropenem showed a binding score of -1.9 kcal/mol, while doripenem showed the binding score of -2.5 kcal/mol respectively. Doripenem, imipenem, and meropenem docking findings with blaOXA-24 confirmed their binding energies. Doripenem had the highest docking energy of -5.5 kcal/mol, meropenem had a binding score of -4.0 kcal/mol, and imipenem had a binding score of -3.9 kcal/mol. PyRx was used to dock the doripenem, imipenem, and meropenem to NMD-1. Docking energies for doripenem were all - 4.0 kcal/mol, whereas meropenem had docking energy of -3.3 kcal/mol and imipenem was -1.50 kcal/mol. To the best of our knowledge the underlying mechanism of phenotypic with genotypic resistance molecular docking regarding carbapenem resistance A. baumannii is unclear. Our molecular docking finds the possible protein targeting mechanism for carbapenem-resistant A.baumannii.

Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil

Chryseobacterium indologenes is a non-glucose-fermenting Gram-negative bacillus. This emerging multidrug resistant opportunistic nosocomial pathogen can cause severe infections in neonates and immunocompromised patients. This study aimed to present the first detailed draft genome sequence of a multidrug-resistant C. indologenes strain isolated from the cerebrospinal fluid of an infant hospitalized at the Neonatal Intensive Care Unit of Brazilian Tertiary Hospital. We first analyzed the susceptibility of C. indologenes strain to different antibiotics using the VITEK 2 system. The strain demonstrated an outstanding resistance to all the antibiotic classes tested, including β-lactams, aminoglycosides, glycylcycline, and polymyxin. Next, C. indologenes was whole-genome-sequenced, annotated using Prokka and Rapid Annotation using Subsystems Technology (RAST), and screened for orthologous groups (EggNOG), gene ontology (GO), resistance genes, virulence genes, and mobile genetic elements using different software tools. The draft genome contained one circular chromosome of 4,836,765 bp with 37.32% GC content. The genomic features of the chromosome present numerous genes related to cellular processes that are essential to bacteria. The MDR C. indologenes revealed the presence of genes that corresponded to the resistance phenotypes, including genes to β-lactamases (bla_IND–13, bla_CIA–3, bla_TEM–116, bla_OXA–209, bla_VEB–15), quinolone (mcbG), tigecycline (tet(X6)), and genes encoding efflux pumps which confer resistance to aminoglycosides (RanA/RanB), and colistin (HlyD/TolC). Amino acid substitutions related to quinolone resistance were observed in GyrA (S83Y) and GyrB (L425I and K473R). A mutation that may play a role in the development of colistin resistance was detected in lpxA (G68D). Chryseobacterium indologenes isolate harbored 19 virulence factors, most of which were involved in infection pathways. We identified 13 Genomic Islands (GIs) and some elements associated with one integrative and conjugative element (ICEs). Other elements linked to mobile genetic elements (MGEs), such as insertion sequence (ISEIsp1), transposon (Tn5393), and integron (In31), were also present in the C. indologenes genome. Although plasmids were not detected, a ColRNAI replicon type and the most resistance genes detected in singletons were identified in unaligned scaffolds. We provided a wide range of information toward the understanding of the genomic diversity of C. indologenes, which can contribute to controlling the evolution and dissemination of this pathogen in healthcare settings.